Higher plants cannot move to a more favorable place when the environmental conditions are changing. To adapt to changes in light, temperature and access to water the plants had to evolve special mechanisms at the molecular level. Post-translational modifications of proteins, like phosphorylation, often serve as “on-and-off” switches in regulation of cellular activity and may affect protein-protein interactions. Photosynthesis in higher plants is regulated by reversible protein phosphorylation events, in a unique light- and redox-controlled system. Several biochemical methods are effectively used for characterization of phosphorylated proteins in photosynthetic membranes. Nevertheless, mass spectrometry is the most effective technique when it comes to identification of exact phosphorylation site(s) in the protein sequence, which is the ultimate evidence of protein phosphorylation. The same tandem mass spectrometry analysis identifies other in vivo post-translational modifications as well, such as acetylation of the N-terminus of mature protein. To study membrane proteins is a challenging project. In the present work the “shaving” of surface-exposed part of the membrane proteins, where phosphorylation occur, is used. In combination with mass spectrometry, this technique does not require the use of radioactive labeling or antibodies. The present work in spinach and Arabidopsis thaliana has identified and characterized several known phosphoproteins, new phosphorylation sites in well-known photosynthetic proteins, as well as two phosphoproteins previously unknown to be present in the photosynthetic membrane. Several photosystem II (PSII) core proteins become phosphorylated in their N-termini (D1, D2, CP43, PsbH), process involved in the regulation of the repair cycle of photo-damaged PSII complexes. The protein-protein interactions between PSII and its light harvesting complex (LHCII) seem to be affected by phosphorylation events in the interface area. In higher plants, phosphorylation sites have been identified in LHCII polypeptides, in one of the proteins (CP29) present in the interface area, as well as in the peripheral TSP9 protein. The TSP9 protein is unique among photosynthetic phosphoproteins, since it is a plant-specific soluble protein that becomes triple-phosphorylated in the middle part of the protein. It is also shown that photosystem I (PSI) is subjected to protein phosphorylation. The extrinsic PSI subunit PsaD becomes phosphorylated in its N-terminus. In addition, the latest characterized subunit of PSI, PsaP, is identified as a phosphoprotein. PsaP is an intrinsic protein assembled on the same side of the PSI complex as LHCII attaches. Several kinases are involved in phosphorylation of photosynthetic proteins, some more specific to PSII core proteins whereas others recognize LHCII proteins better. The STN8 kinase does not phosphorylate LHCII proteins, but is involved in the phosphorylation of the PSII core proteins D1, D2, CP43 and PsbH. STN8 is light-activated and is also specific in phosphorylation of threonine-4 (Thr-4) in the PsbH protein, but only after another kinase has phosphorylated Thr-2 first. A common feature of all kinases in plant photosynthetic membranes is the specificity for Thr residues and that the phosphorylation reactions occur in the N-terminal sequence of the proteins, except for the TSP9 protein. Nowadays, research is on the way to solve the complex network of regulation of photosynthetic activity via protein phosphorylation, but far more efforts are needed to get a complete view of the importance of all phosphorylation events and enzymatic specificity.

The HIV-1 transactivator of transcription (Tat) is a protein essential for both viral gene expression and virus replication. Tat is an RNA-binding protein that, in cooperation with host cell factors cyclin T1 and cyclin-dependent kinase 9, regulates transcription at the level of elongation. Tat also interacts with numerous other intracellular and extracellular proteins, and is implicated in a number of pathogenic processes. The Tat protein is encoded by two exons and is 101 residues in length. The first exon encodes a 72-residue molecule that activates transcription with the same proficiency as the full-length protein. The physico-chemical properties of Tat make it a particularly challenging target for structural studies: Tat contains seven cysteine residues, six of which are essential for transactivation, and is highly susceptible to oxidative cross-linking and aggregation. In addition, a basic segment (residues 48-57) gives the protein a high net positive charge of +12 at pH 7, endowing it with a high affinity for anionic polymers and surfaces. In order to study the structure of Tat, both alone and in complex with partner molecules, we have developed a system for the bacterial expression and purification of polyhistidine-tagged and isotopically enriched (in 15N and 15N /13C) recombinant HIV-1 Tat1-72 (BH10 isolate) that yields large amounts of protein. These preparations have facilitated the assignment of 95% of the non-proline backbone resonances using heteronuclear 3-dimensional nuclear magnetic resonance (NMR) spectroscopy. Analysis by mass spectrometry and NMR demonstrate that the cysteine-rich Tat protein is unambiguously reduced and monomeric in aqueous solution at pH 4. NMR chemical shifts and coupling constants suggest that it exists in a disordered conformation. Line broadening and multiple peaks in the cysteine-rich and core regions suggest that transient folding occurs in two of the five sequence domains. NMR relaxation parameters were measured and analysed by spectral density and model-free approaches both confirming the lack of structure throughout the length of the molecule. The absence of a fixed conformation and the observation of fast dynamics are consistent with the ability of the Tat protein to interact with a wide variety of proteins and nucleic acid lending further support to the concept that Tat exists as an intrinsically disordered protein. / October 2007

The HIV-1 transactivator of transcription (Tat) is a protein essential for both viral gene expression and virus replication. Tat is an RNA-binding protein that, in cooperation with host cell factors cyclin T1 and cyclin-dependent kinase 9, regulates transcription at the level of elongation. Tat also interacts with numerous other intracellular and extracellular proteins, and is implicated in a number of pathogenic processes. The Tat protein is encoded by two exons and is 101 residues in length. The first exon encodes a 72-residue molecule that activates transcription with the same proficiency as the full-length protein. The physico-chemical properties of Tat make it a particularly challenging target for structural studies: Tat contains seven cysteine residues, six of which are essential for transactivation, and is highly susceptible to oxidative cross-linking and aggregation. In addition, a basic segment (residues 48-57) gives the protein a high net positive charge of +12 at pH 7, endowing it with a high affinity for anionic polymers and surfaces. In order to study the structure of Tat, both alone and in complex with partner molecules, we have developed a system for the bacterial expression and purification of polyhistidine-tagged and isotopically enriched (in 15N and 15N /13C) recombinant HIV-1 Tat1-72 (BH10 isolate) that yields large amounts of protein. These preparations have facilitated the assignment of 95% of the non-proline backbone resonances using heteronuclear 3-dimensional nuclear magnetic resonance (NMR) spectroscopy. Analysis by mass spectrometry and NMR demonstrate that the cysteine-rich Tat protein is unambiguously reduced and monomeric in aqueous solution at pH 4. NMR chemical shifts and coupling constants suggest that it exists in a disordered conformation. Line broadening and multiple peaks in the cysteine-rich and core regions suggest that transient folding occurs in two of the five sequence domains. NMR relaxation parameters were measured and analysed by spectral density and model-free approaches both confirming the lack of structure throughout the length of the molecule. The absence of a fixed conformation and the observation of fast dynamics are consistent with the ability of the Tat protein to interact with a wide variety of proteins and nucleic acid lending further support to the concept that Tat exists as an intrinsically disordered protein.

The HIV-1 transactivator of transcription (Tat) is a protein essential for both viral gene expression and virus replication. Tat is an RNA-binding protein that, in cooperation with host cell factors cyclin T1 and cyclin-dependent kinase 9, regulates transcription at the level of elongation. Tat also interacts with numerous other intracellular and extracellular proteins, and is implicated in a number of pathogenic processes. The Tat protein is encoded by two exons and is 101 residues in length. The first exon encodes a 72-residue molecule that activates transcription with the same proficiency as the full-length protein. The physico-chemical properties of Tat make it a particularly challenging target for structural studies: Tat contains seven cysteine residues, six of which are essential for transactivation, and is highly susceptible to oxidative cross-linking and aggregation. In addition, a basic segment (residues 48-57) gives the protein a high net positive charge of +12 at pH 7, endowing it with a high affinity for anionic polymers and surfaces. In order to study the structure of Tat, both alone and in complex with partner molecules, we have developed a system for the bacterial expression and purification of polyhistidine-tagged and isotopically enriched (in 15N and 15N /13C) recombinant HIV-1 Tat1-72 (BH10 isolate) that yields large amounts of protein. These preparations have facilitated the assignment of 95% of the non-proline backbone resonances using heteronuclear 3-dimensional nuclear magnetic resonance (NMR) spectroscopy. Analysis by mass spectrometry and NMR demonstrate that the cysteine-rich Tat protein is unambiguously reduced and monomeric in aqueous solution at pH 4. NMR chemical shifts and coupling constants suggest that it exists in a disordered conformation. Line broadening and multiple peaks in the cysteine-rich and core regions suggest that transient folding occurs in two of the five sequence domains. NMR relaxation parameters were measured and analysed by spectral density and model-free approaches both confirming the lack of structure throughout the length of the molecule. The absence of a fixed conformation and the observation of fast dynamics are consistent with the ability of the Tat protein to interact with a wide variety of proteins and nucleic acid lending further support to the concept that Tat exists as an intrinsically disordered protein.

O aumento na demanda por alimentos saudáveis e minimamente processados impulsiona a busca por novos agentes antimicrobianos. As bacteriocinas são peptídeos produzidos via ribossomo por algumas espécies de bactérias, podendo ser usadas na conservação e garantia da inocuidade de alimentos, não apresentando as possíveis ações tóxicas de conservadores clássicos amplamente utilizados na indústria alimentícia. Carnobacterium maltaromaticum C2 foi isolado de peixe defumado brasileiro (Surubim, Pseudoplatystoma sp.), e apresenta grande capacidade de inibir a multiplicação de Listeria monocytogenes, demonstrando seu potencial para aplicação na bioconservação de alimentos. Em estudos anteriores, foi demonstrado que essa linhagem bacteriana produz compostos antimicrobianos de origem proteica. Neste trabalho, foram avaliados aspectos gerais da produção de bacteriocinas por C. maltaromaticum C2, assim como sua purificação e caracterização. C. maltaromaticum C2 produz bacteriocinas entre 5 e 25ºC, com ótimo entre 20 e 25ºC. Do mesmo modo, a produção desses compostos foi maior em caldo APT (All purpose Tween), entretanto para as etapas de purificação foram utilizados o caldo BHI (Brain heart infusion) e CAA (Casamino acids), por causarem menos interferência no processo. Lactobacillus sakei e L. monocytogenes foram inibidos pelas bacteriocinas parcialmente purificadas produzidas por C. maltaromaticum C2, e seus peptídeos antimicrobianos apresentaram moderada estabilidade térmica quando expostos a 100ºC por 30 minutos. Foram utilizadas duas técnicas para extração e purificação das bacteriocinas, a técnica de adsorção-dessorção às células produtoras, e a purificação com a resina XAD-16, baseada em interações hidrofílicas e hidrofóbicas com os peptídeos, seguida de extração em fase sólida, sendo que este último processo de purificação resultou em um extrato com alto teor de pureza, como observado durante as análises por cromatografia líquida de alta eficiência em coluna de fase reversa. Com o auxílio de técnicas de espectrometria de massas, foi detectado nos extratos obtidos a presença das carnobacteriocinas BM1 e B1, assim como o peptídeo antimicrobiano CbnX. Este trabalho é pioneiro na purificação de CbnX, pois anteriormente havia somente a descrição de seu gene, mas não havia sido descrita a purificação do peptídeo. Neste sentido, a linhagem estudada é única até o momento e poderá favorecer estudos de expressão gênica de bacteriocinas, bem como a otimização de processos de bioconservação. / The high demand for healthy and minimally processed foods has increased the search for new antimicrobial agents. Bacteriocins are ribosomally synthesized peptides produced by some bacteria, and are useful for biopreservation and food safety, without the possible toxic effects of classical preservatives widely used in food industry. Carnobacterium maltaromaticum C2 was isolated from Brazilian smoked fish (Surubim, Pseudoplatystoma sp.), and it inhibits Listeria monocytogenes, an important foodborne pathogen. In previous studies, it was demonstrated that this bacterial strain produces bacteriocins. In this study, general aspects of the production of bacteriocins by C. maltaromaticum C2 were evaluated, as well as their purification and characterization. C. maltaromaticum C2 produces bacteriocins between 5 and 25ºC, with the optimum incubation temperature between 20 and 25ºC. Similarly, the production of these compounds was higher in APT (All-purpose Tween) broth. However, for the purification steps, BHI (Brain heart infusion) broth and CAA (Casamino acids) broth were used due to their low interference with the processes. Lactobacillus sakei and L. monocytogenes were inhibited by the partially purified bacteriocins produced C. maltaromaticum C2, and their antimicrobial peptides showed moderate thermal stability when tested at 100ºC by 30 minutes. Two techniques for extraction and purification of the antimicrobial peptides were used, the adsorption-desorption of bacteriocins to the producer cells, and the purification with XAD-16 resin, based on hydrophilic and hydrophobic interactions with the peptides, followed by a step of solid phase extraction. The latter resulted in an extract with high purity, as observed by the analysis with reverse-phase high performance liquid chromatography. With mass spectrometry techniques, carnobacteriocins BM1 and B1 were detected, as well as the antimicrobial peptide CbnX. This is an innovative work because the purification of CbnX had never been reported, except its gene. In this respect, this C. maltaromaticum strain is unique until this moment, and may promote researches on gene expression, as well the optimization of biopreservation processes.

O aumento na demanda por alimentos saudáveis e minimamente processados impulsiona a busca por novos agentes antimicrobianos. As bacteriocinas são peptídeos produzidos via ribossomo por algumas espécies de bactérias, podendo ser usadas na conservação e garantia da inocuidade de alimentos, não apresentando as possíveis ações tóxicas de conservadores clássicos amplamente utilizados na indústria alimentícia. Carnobacterium maltaromaticum C2 foi isolado de peixe defumado brasileiro (Surubim, Pseudoplatystoma sp.), e apresenta grande capacidade de inibir a multiplicação de Listeria monocytogenes, demonstrando seu potencial para aplicação na bioconservação de alimentos. Em estudos anteriores, foi demonstrado que essa linhagem bacteriana produz compostos antimicrobianos de origem proteica. Neste trabalho, foram avaliados aspectos gerais da produção de bacteriocinas por C. maltaromaticum C2, assim como sua purificação e caracterização. C. maltaromaticum C2 produz bacteriocinas entre 5 e 25ºC, com ótimo entre 20 e 25ºC. Do mesmo modo, a produção desses compostos foi maior em caldo APT (All purpose Tween), entretanto para as etapas de purificação foram utilizados o caldo BHI (Brain heart infusion) e CAA (Casamino acids), por causarem menos interferência no processo. Lactobacillus sakei e L. monocytogenes foram inibidos pelas bacteriocinas parcialmente purificadas produzidas por C. maltaromaticum C2, e seus peptídeos antimicrobianos apresentaram moderada estabilidade térmica quando expostos a 100ºC por 30 minutos. Foram utilizadas duas técnicas para extração e purificação das bacteriocinas, a técnica de adsorção-dessorção às células produtoras, e a purificação com a resina XAD-16, baseada em interações hidrofílicas e hidrofóbicas com os peptídeos, seguida de extração em fase sólida, sendo que este último processo de purificação resultou em um extrato com alto teor de pureza, como observado durante as análises por cromatografia líquida de alta eficiência em coluna de fase reversa. Com o auxílio de técnicas de espectrometria de massas, foi detectado nos extratos obtidos a presença das carnobacteriocinas BM1 e B1, assim como o peptídeo antimicrobiano CbnX. Este trabalho é pioneiro na purificação de CbnX, pois anteriormente havia somente a descrição de seu gene, mas não havia sido descrita a purificação do peptídeo. Neste sentido, a linhagem estudada é única até o momento e poderá favorecer estudos de expressão gênica de bacteriocinas, bem como a otimização de processos de bioconservação. / The high demand for healthy and minimally processed foods has increased the search for new antimicrobial agents. Bacteriocins are ribosomally synthesized peptides produced by some bacteria, and are useful for biopreservation and food safety, without the possible toxic effects of classical preservatives widely used in food industry. Carnobacterium maltaromaticum C2 was isolated from Brazilian smoked fish (Surubim, Pseudoplatystoma sp.), and it inhibits Listeria monocytogenes, an important foodborne pathogen. In previous studies, it was demonstrated that this bacterial strain produces bacteriocins. In this study, general aspects of the production of bacteriocins by C. maltaromaticum C2 were evaluated, as well as their purification and characterization. C. maltaromaticum C2 produces bacteriocins between 5 and 25ºC, with the optimum incubation temperature between 20 and 25ºC. Similarly, the production of these compounds was higher in APT (All-purpose Tween) broth. However, for the purification steps, BHI (Brain heart infusion) broth and CAA (Casamino acids) broth were used due to their low interference with the processes. Lactobacillus sakei and L. monocytogenes were inhibited by the partially purified bacteriocins produced C. maltaromaticum C2, and their antimicrobial peptides showed moderate thermal stability when tested at 100ºC by 30 minutes. Two techniques for extraction and purification of the antimicrobial peptides were used, the adsorption-desorption of bacteriocins to the producer cells, and the purification with XAD-16 resin, based on hydrophilic and hydrophobic interactions with the peptides, followed by a step of solid phase extraction. The latter resulted in an extract with high purity, as observed by the analysis with reverse-phase high performance liquid chromatography. With mass spectrometry techniques, carnobacteriocins BM1 and B1 were detected, as well as the antimicrobial peptide CbnX. This is an innovative work because the purification of CbnX had never been reported, except its gene. In this respect, this C. maltaromaticum strain is unique until this moment, and may promote researches on gene expression, as well the optimization of biopreservation processes.

The health and viability of cells and tissues in the human body depend on the functional integrity of proteins. A small number of long-lived proteins, including the crystallins in the lens of the eye, evade protein turnover, a typical cellular mechanism for repair and regeneration, and remain extant throughout life. The cumulative effect of post-translational modifications on the structure, function, and conformation of these long-lived proteins records the history of molecular aging in an individual. Along with absence of protein turnover, the optical accessibility, transparency, and age-related spatial order make the lens an ideal target for in vivo assessment of molecular aging. Accordingly, this doctoral thesis investigated the hypothesis that age-related perturbations that alter the protein environment in the human lens can be detected and monitored as a quantitative biomarker of molecular aging detectable by quasi-elastic light scattering (QLS). To test this hypothesis, QLS was applied in vitro and in vivo to study time-dependent changes in lens proteins. Water-soluble human lens protein extract was used in vitro as a model system that mimics the lens fiber cell cytoplasm. The effects of long-term incubation (nearly one year, proxy for aging), oxidative stress, ionizing radiation, metal-protein and pathogenic protein-protein interactions were investigated by QLS as a function of time. In vitro results were validated by protein gel electrophoresis and transmission electron microscopy. In vivo, age-dependent changes in lens proteins were assessed in healthy subjects across a broad age-range (5–61 years of age). Pathogenic protein aggregation in the lens was examined in vivo using Down syndrome (DS) subjects, a common chromosomal disease associated with an age-related Alzheimer’s disease (AD)-linked lens phenotype. Results obtained from the in vitro studies noted, for the first time, QLS detection of long-term supramolecular changes in a complex lens protein model system. Our FDA-approved QLS device was successful in assessing age-dependent lens protein changes in a clinical study at Boston Children’s Hospital (BCH). In two landmark studies conducted at BCH, we detected statistically significant AD-related lens protein changes in DS subjects aged 10–20 years, when compared with age-matched controls. These studies are the first clinical application of QLS in DS, and demonstrate protein changes in DS earlier than any previously reported studies. Due to the discrepancy in chronological and biological age and the lack of an objective index for the latter, we propose the application of QLS in the human lens as a quantitative biomarker of molecular aging.

<p>Curiosity is a powerful tool, and combined with the ability to observe the natural world, grants humankind an unique opportunity, the opportunity to wonder why. Why do things exist?, why do they do the things they do?, why is this even possible?</p> <p>Research in our lab is focused on the basic understanding and potential application of biological materials, in particular, biological adhesives produced by marine organisms such as oysters. Oysters produce a cement-like material that is able to withstand the dynamic conditions found in coastal environments. The focus of this dissertation is to lay the basis of the characterization of new biological materials by observing and analyzing its physical properties, to measure the performance of the material in natural conditions and finally to identify the basic components that give the material the properties that we observe. The end goal of this project is to understand the properties of this material so we are able to develop a synthetic system that is able to imitate, as close as possible, what we find in nature. These results, and more importantly, the new questions that emerge from this research, provide a first look at the adhesive system of oysters leading the way to new discoveries in the future.</p>

The Sun is the ultimate energy source on Earth. Photosynthetic organisms are able to catalyze the conversion of solar energy to chemical energy by a reaction called photosynthesis. In plants, this process occurs inside a green organelle called the chloroplast. The protein complexes involved in the photosynthetic light reactions are situated in the thylakoid membrane, which encloses a tiny space called lumen. The Peptidyl-Prolyl cis-trans Isomerase (PPIase) family is the most abundant protein family in the thylakoid lumen. The three PPIase subfamilies, cyclophilins, FKBPs (FK506 binding proteins) and parvulins form a group by their enzymatic activity despite lack of sequence similarity between the subfamilies. Cyclophilins and FKBPs, collectively called immunophilins, were originally discovered as the targets of the immunosuppressive drugs cyclosporine A and FK506, respectively. By suppressing the immune response in humans, these immunophilin-drug complexes revolutionized the field of organ transplantation by preventing graft rejection. Cis-trans isomerization of peptide bonds preceding the amino acid proline is the rate-limiting step of protein folding and several immunophilins have been shown to be important for catalysis of protein folding in vivo. PPIases have been found to be part of large protein complexes as well as in functions such as signalling, protein secretion, RNA processing and cell cycle control. A picture is therefore emerging in which the actual interaction between the PPIase and its target is perhaps more important than the PPIase activity. In the present work, PPIases have been characterized in the chloroplast thylakoid lumen of Spinacia oleracea (spinach) and Arabidopsis thaliana (Arabidopsis). The most active PPIase in the spinach lumen was identified as the cyclophilin TLP20. AtCYP20-2, the Arabidopsis homologue of TLP20, was found to be upregulated at high light and attached to the thylakoid membrane, more precisely to the outer regions of photosystem II supercomplexes. In Arabidopsis, up to 5 cyclophilins and 11 FKBPs were predicted to reside in the lumen. Of these 16 immunophilins, only 2 were identified as active PPIases and significant differences were observed between the two plant species. AtCYP20-2, like TLP20, is an active isomerase although AtFKBP13 is the most active PPIase in the lumen of Arabidopsis. Mutant Arabidopsis plants deficient in AtCYP20-2 displayed no phenothypical changes or decrease in total lumenal PPIase activity. Being the only active PPIase in the mutants, the redox sensitive AtFKBP13 is proposed to compensate for the lack of AtCYP20-2 by oxidative activation. In agreement with the experimental data, the sequence analyses of catalytic domains of lumenal immunophilins demonstrate that only AtCYP20-2 and AtFKBP13 possess the amino acids found essential for PPIase activity in earlier studies of human cyclophilin A and FKBP12. It is concluded that with the exception of AtCYP20-2 and AtFKBP13 most immunophilins in the lumen of Arabidopsis lost their PPIase activity on peptide substrates and developed other specialized functions.

No description available.